Sorghum bicolor vs Hordeum vulgare LastZ Results

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Sorghum bicolor (Sorghum bicolor, Sorghum_bicolor_NCBIv3) and Hordeum vulgare (Hordeum vulgare, Hv_IBSC_PGSB_v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Sorghum bicolor was used as the reference species. After running LastZ, the raw LastZ alignment blocks are chained according to their location in both genomes. During the final netting process, the best sub-chain is chosen in each region on the reference species.

Results

Number of alignment blocks: 377,368

Genome coverage (bp) Coding exon coverage (bp)
Sorghum bicolor

Uncovered: 620,667,269 out of 708,735,318
Covered: 88,068,049 out of 708,735,318

Uncovered: 5,005,645 out of 39,785,927
Matches: 25,327,212 out of 39,785,927
Mismatches: 8,446,153 out of 39,785,927
Insertions: 1,006,917 out of 39,785,927

Hordeum vulgare

Uncovered: 4,688,235,563 out of 4,833,907,081
Covered: 145,671,518 out of 4,833,907,081

Uncovered: 6,142,469 out of 44,392,268
Matches: 28,893,146 out of 44,392,268
Mismatches: 8,381,292 out of 44,392,268
Insertions: 975,361 out of 44,392,268

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
Masking count (M)
Seed and Transition value (T)1
Scoring matrix (Q)
Default:
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91
Other parameters (other)--ambiguous=iupac

Chunking parameters

Sorghum bicolor Hordeum vulgare
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}